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Genomics |
Department of Biology, University of California at San Diego, La Jolla, CA 92093-0116, USA1
Author for correspondence: Milton H. Saier, Jr. Tel: +1 858 534 4084. Fax: +1 858 534 7108. e-mail: msaier{at}ucsd.edu
In this paper an analysis of 175 currently sequenced transport proteins that comprise the amino acid/polyamine/organocation (APC) superfamily is reported. Members of this superfamily fall into 10 well-defined families that are either prokaryote specific, eukaryote specific or ubiquitous. Most of these proteins exhibit 12 probable transmembrane spanners (TMSs), but members of two of these families deviate from this pattern, exhibiting 10 and 14 TMSs. All members of these families are tabulated, their functional properties are reviewed and phylogenetic/sequence analyses define the evolutionary relationships of the proteins to each other. Evidence is presented that the APC superfamily may include two other currently recognized families that exhibit greater degrees of sequence divergence from APC superfamily members than do the proteins of the 10 established families from each other. At least some of the protein members of these two distantly related families exhibit 11 established TMSs. Altogether, the APC superfamily probably includes 12 currently recognized families with members that exhibit exclusive specificity for amino acids and their derivatives but which can possess 10, 11, 12 or 14 TMSs per polypeptide chain.
Keywords: amino acids, transport, evolution, superfamily, secondary carriers
Abbreviations: AAAP, amino acid/auxin permease; AAT, amino acid transporter; ABT, archaeal/bacterial transporter; ACT, amino acid/choline transporter; APA, basic amino acid/polyamine antiporter; APC, amino acid/polyamine/organocation; CAT, cationic amino acid transporter; EAT, ethanolamine transporter; GGA, glutamate:GABA antiporter; HAAAP, hydroxy/aromatic amino acid permease; LAT, L-type amino acid transporter; SGP, spore germination protein; TC, transporter classification; TMS, transmembrane 
-helical spanner; YAT, yeast amino acid transporter
a 
Present address: The Institute for Genomic Research (TIGR), 9712 Medical Center Drive, Rockville, MD 20850, USA.
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